well the first thing Cisco will tell is that QoS over the Internet is not supported. There are some strides being made with Cisco Powered Networks though. Just remember that you are at the mercy of the Internet. That being said, I am running VoIP over VPN over the Internet myself. I am doing QoS on the origination point and the central office but at the mercy of the Internet gods everywhere in between. Right now I have it restricted to internal usa only and will test for about a year to see if I can open this up to customer contact. As far as routing the voice calls over the VPN alot depends on your equipment. I am running a 3002 behind a 2650XM at each remote site and a 3005 as the head-end device. works like a charm. PLeanty of other ways to set this up though. E me if you have any questions.
